# issues with qiime2-amplicon-2024.2 for core-metrics-phylogenetic
**URL:** https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161
**Category:** User Support
**Created:** [May 10, 2024, 2:51pm UTC](https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161 "2024-05-10T14:51:22Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@1111](https://forum.qiime2.org/u/1111)
#### Post date: [May 10, 2024, 2:51pm UTC](https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161/1 "2024-05-10T14:51:22Z")
(qiime2-amplicon-2024.2) [XYB@Dulab fastq]$ qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree-withoutPRJNA445346.qza --i-table table-filter-contam-no-archaea-eukaryota-withouPRJNA445346.qza --p-sampling-depth 60000 --m-metadata-file paired\_metadata\_without\_PRJNA445346.tsv --output-dir core-metric-results --verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
faithpd -i /tmp/qiime2/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom -t /tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-113rtk76
Compute failed in faith\_pd\_one\_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely).
Traceback (most recent call last):
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 520, in **call**
results = self.\_execute\_action(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/commands.py", line 586, in \_execute\_action
results = action(\*\*arguments)
File "", line 2, in core\_metrics\_phylogenetic
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable\_executor_
outputs = self.\_callable(scope.ctx, \*\*view\_args)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity/\_core\_metrics.py", line 65, in core\_metrics\_phylogenetic
faith\_pd\_vector, = faith\_pd(table=cr.rarefied\_table,
File "", line 2, in faith\_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/context.py", line 143, in deferred\_action
return action\_obj.\_bind(
File "", line 2, in faith\_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "", line 2, in faith\_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 75, in \_validate\_tables
return wrapped\_function(\*args, \*\*kwargs)
File "", line 2, in faith\_pd
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 118, in \_validate\_requested\_cpus
return wrapped\_function(\*bound\_arguments.args, \*\*bound\_arguments.kwargs)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/alpha.py", line 54, in faith\_pd
\_omp\_cmd\_wrapper(threads, cmd)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 134, in \_omp\_cmd\_wrapper
return \_run\_external\_cmd(cmd, verbose=verbose, env=env)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 128, in \_run\_external\_cmd
return subprocess.run(cmd, check=True, env=env)
File "/data/home/XYB/01.software/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['faithpd', '-i', '/tmp/qiime2/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom', '-t', '/tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-113rtk76']' returned non-zero exit status 1.
Plugin error from diversity:
Command '['faithpd', '-i', '/tmp/qiime2/XYB/data/e1bfdd46-1e1c-44d3-8de5-cd2e09813951/data/feature-table.biom', '-t', '/tmp/qiime2/XYB/data/2d5ad368-de70-45ea-9869-a890013a3200/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-113rtk76']' returned non-zero exit status 1.
See above for debug info.
---
### Author:  [@timanix](https://forum.qiime2.org/u/timanix)
#### Post date: [May 10, 2024, 6:05pm UTC](https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161/2 "2024-05-10T18:05:16Z")
Hello!
> [@1111](#):
>
> Compute failed in faith\_pd\_one\_off: Table observation IDs are not a subset of the tree tips. This error can also be triggered if a node name contains a single quote (this is unlikely).
Here is a key part. Looks like you have some features in the table that are missing in the tree you provided. Double check your filtering steps to make sure that all features from the table are present in tree.
Best,
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### Author:  [@1111](https://forum.qiime2.org/u/1111)
#### Post date: [May 18, 2024, 3:01pm UTC](https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161/3 "2024-05-18T15:01:51Z")
Dear timanix,
Thanks for your help! I checked the filter steps and figured out the mistakes since I did not keep the same conditions for the feature table and feature sequences 😅 uh.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 18, 2024, 9:02pm UTC](https://forum.qiime2.org/t/issues-with-qiime2-amplicon-2024-2-for-core-metrics-phylogenetic/30161/4 "2024-06-18T21:02:08Z")
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